Mommsen wrote a biography of Max Weber in 1959. His main areas of expertise were in 19th century-20th century British and German history. His interests were wide-ranging and he wrote about diplomatic, social, intellectual, and economic history. Mommsen championed a Sonderweg ("special path") interpretation of German history. Echoing the views of Hans-Ulrich Wehler and Fritz Fischer, he argued that 19th century Germany was only partially modernized. Economic modernization was not accompanied by political modernization. Much of Mommsen's comparative studies of British and German history concern why, in his view, the British had both a political and economic modernization while the Germans had only the latter. An Anglophile, Mommsen very much enjoyed teaching and living in Britain.

In Mommsen's view, the foreign policy of the Second Reich was driven by domestic concerns as the German elite sought distractions abroad to hold off demands for democracy at home. This argument places Mommsen in the Primat der Innenpolitik (primacy of domestic politics) school against the traditional Primat der Aussenpolitik (primacy of foreign politics) school as an explanation for foreign policy. For Mommsen, the major responsibility for the outbreak of the First World War rests on Germany's shoulders. Furthermore, the November Revolution of 1918 did not go far enough and allowed the pre-1918 elite to continue to dominate German life, thus leading inevitably to the Third Reich. Mommsen has written books condemning appeasement.

In the Historikerstreit (historians' dispute), Mommsen took the position that the Holocaust was a uniquely evil event that should not be compared to Stalinist terror in the Soviet Union. In an article entitled "Neither Denial nor Forgetfulness Will Free Us" first published in the Frankfurter Rundschau on December 1, 1986, Mommsen argued that Historikerstreit was a result of the failures of modern society[1] Mommsen argued that in the prosperous 1950s–60s, most Germans were happy to forget about their recent past, and looked forward to a brighter future[1] Starting with the oil shock of the early 1970s and the rise of fundamentalist Islam in the late 1970s, Mommsen argued that the idea of a progressively better future was discredited, leading to a pessimistic public mood, and the a renewed interest in history[2] This had occurred in tandem in a period when German historians had started to make a more critical examination of their recent past[3] As a result at the precise mood when the public demanded a past that could make them feel good about being Germans, German historians came under attack for not writing the sort of history the public wanted[4] Mommsen argued that the work of those like Ernst Nolte was intended to provide the sort of history that would allow Germans feel good about being Germans by engaging in “…an explanatory strategy that…will be seen as a justification of National Socialist crimes by all those who are still under the influence of the extreme anti-Soviet propaganda of National Socialism"[5] Mommsen charged that Ernst Nolte was attempting egregiously to whitewash the German past.[6] Mommsen argued that Nolte was attempting a "justification" of Nazi crimes and making "inappropriate" comparisons of the Holocaust with other genocides.[7] Mommsen wrote about Andreas Hillgruber's demands that historians identified with the “justified” German defence of the Eastern Front that:

“Andreas Hillgruber recently attempted to accord a relative historical justification to the Wehrmacht campaign in the East and the desperate resistance of the army in the East after the summer of 1944. He argued that the goal was to prevent the German civilian population from falling into the hands of the Red Army. However, the chief reason, he argued, was that the defense of German cities in the East had become tantamount to defending Western civilization. In light of the Allied war goals, which independent of Stalin’s final plans, envisioned breaking up Prussia, and destroying the defensive position of a strong, Prussian-led Central European state that could serve as a bulwark against Bolshevism, the continuation of the war in the East was justified from the viewpoint of those involved. It was, as Hillgruber’s argument would have it, also justified even from today’s standpoint, despite the fact that prolonging the war in the East mean that the gigantic murder machinery of the Holocaust would be allowed to continue to run. All this, the essay argued, was justified as long as the fronts held. Hillgruber’s essay is extremely problematic when viewed from the perspective of a democratically constituted community that orients itself towards Western moral and political standards.

There is no getting around the bitter truth that the defeat of National Socialist Germany was not only in the interest of the peoples who were bulldozed by Hitler’s war and of the peoples who were selected by his henchmen for annihilation or oppression or exploitation-it was also in the interest of the Germans. According, parts of the gigantic scenery of the Second World War were, at least as far as we were concerned, totally senseless, even self-destructive. We cannot escape this bitter truth by assigning partial responsibility to other partners who took part in the war”[8]

Mommsen ended his essay by writing that the Federal Republic marked the end of the Sonderweg, and Germans should accept the “burden” of the past as way of inspiring them to do better in the future[9]

In 1998, several younger German historians criticized Mommsen for not denouncing the Nazi past of his mentors while a university student in the 1950s.